migrated split biopieces

git-svn-id: http://biopieces.googlecode.com/svn/trunk@400 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..47e2947747c7db594268f427e3b471d6f3a7d410 100755 (executable)
--- a/bp_bin/split_bed
+++ b/bp_bin/split_bed
@@ -1,6 +1,101 @@
-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Split BED entries into overlapping windows.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $new_record, $i );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'window_size', short => 'w', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => 0 },
+        { long => 'step_size',   short => 's', type => 'uint', mandatory => 'no', default => 1,  allowed => undef, disallowed => 0 },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+    {
+        $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
+
+        for ( $i = 0; $i < $record->{ "BED_LEN" } - $options->{ "window_size" }; $i += $options->{ "step_size" } )
+        {
+            $new_record->{ "REC_TYPE" } = "BED";
+            $new_record->{ "CHR" }      = $record->{ "CHR" };
+            $new_record->{ "CHR_BEG" }  = $record->{ "CHR_BEG" } + $i;
+            $new_record->{ "CHR_END" }  = $record->{ "CHR_BEG" } + $i + $options->{ "window_size" };
+            $new_record->{ "BED_LEN" }  = $options->{ "window_size" };
+            $new_record->{ "Q_ID" }     = $record->{ "Q_ID" } . "_$i";
+            $new_record->{ "SCORE" }    = $record->{ "SCORE" };
+            $new_record->{ "STRAND" }   = $record->{ "STRAND" };
+
+            Maasha::Biopieces::put_record( $new_record, $out );
+        }
+    }
+    else
+    {
+        Maasha::Biopieces::put_record( $record, $out );
+    }
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    $run_time_beg = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::log_biopiece();
+}
+
+
+END
+{
+    Maasha::Biopieces::close_stream( $in );
+    Maasha::Biopieces::close_stream( $out );
+
+    $run_time_end = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
 
-use Maasha::BioRun;

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..93ed6c72f1875475cfd4b80ac4fdba206f1f6491 100755 (executable)
--- a/bp_bin/split_seq
+++ b/bp_bin/split_seq
@@ -1,6 +1,107 @@
-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Split sequences in the stream into overlapping subsequences.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $new_record, $i, $subseq, %lookup );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'word_size', short => 'w', type => 'uint', mandatory => 'no', default => 7,     allowed => undef, disallowed => 0 },
+        { long => 'uniq',      short => 'u', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+    {
+        for ( $i = 0; $i < length( $record->{ "SEQ" } ) - $options->{ "word_size" } + 1; $i++ )
+        {
+            $subseq = substr $record->{ "SEQ" }, $i, $options->{ "word_size" };
+
+            if ( $options->{ "uniq" } and not $lookup{ $subseq } )
+            {
+                $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
+                $new_record->{ "SEQ" }      = $subseq;
+
+                Maasha::Biopieces::put_record( $new_record, $out );
+
+                $lookup{ $subseq } = 1;
+            }
+            else
+            {
+                $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
+                $new_record->{ "SEQ" }      = $subseq;
+
+                Maasha::Biopieces::put_record( $new_record, $out );
+            }
+        }
+    }
+    else
+    {
+        Maasha::Biopieces::put_record( $record, $out );
+    }
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    $run_time_beg = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::log_biopiece();
+}
+
+
+END
+{
+    Maasha::Biopieces::close_stream( $in );
+    Maasha::Biopieces::close_stream( $out );
+
+    $run_time_end = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
 
-use Maasha::BioRun;